SCOM R2 agent removed but stays in Computer field under monitoring

Question

We have servers that needs retired, so I uninstall from the console and the servers disappear from the agent managed view. But if you look under computers in the monitoring view the server is still there. When we were on SP1 we had a similar issue and i contacted MS and we got a script to clear it out out of the database (Orphaned Servers)
now that we are on R2 it seems the script doesnt work because it can not locate the name..any suggestion on this
agent manage and computers are off by 22 when they should be the same

Answer 1

Hi I have the same problem.
I have lot of machines in the computer view which are not available in the Agent managed view. that machine was deleted more than 2 weeks ago.
We found the following on the net:
http://www.experts-exchange.com/Microsoft/Server_Applications/Q_26893576.html
You will need to remove the objects from the Database. This is fairly easy to do. Here are the steps that i use when i have this issue.
System Center Operations Manager 2007 stores all "entities" it "manages" in the BaseManagedEntity table in the Operational database (named "OperationsManager", by default). This is the place where we will be manually telling SCOM that this computer does
not exist anymore. There's a column called "IsDeleted" that stores if the agent was removed.
1. Connect to the SCOM SQL server and open SQL Management studio
2. Right click on OperationsManager database and select new query
3. Run the following query in the right window  to see the status of
ALL computers in SCOM
SELECT * FROM dbo.[BasemanagedEntity] where FullName Like '%Windows.Computer%'
4. To see the status of a specific computer in SCOM (replace the text "fqdn" with the server name)
SELECT * FROM dbo.[BasemanagedEntity] where FullName Like '%Windows.Computer%' and Name Like '%FQDN.of.my.computer%'
5. In the results scroll to the right to find the "IsDeleted" column. 0(Zero) means the database does not know the computer has been deleted. If it is zero then we will run the next command to change it to 1 (one)
replace the text "fqdn" with the server name
UPDATE dbo.[BasemanagedEntity] SET IsDeleted = 1 where FullName Like '%Windows.Computer%' and Name Like '%FQDN.of.my.computer%' 
Going back to the Operations Console to the Monitoring & Computer section, shows us that the computer does not show in the list already. It will still take some time before it really gets deleted in the database, but visually you are already set.
(Do note that the machine and its child objects like disk and CPU are still there in the Data Warehouse. This will stay there until that expired there also; which is 360 days by default).